Variant report

Variant	rs2867919
Chromosome Location	chr4:76403289-76403290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10518140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs11099546	0.86[EUR][1000 genomes]
rs11722278	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11727259	0.90[EUR][1000 genomes]
rs11727806	0.82[AFR][1000 genomes]
rs11727923	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11729106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11731477	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12644911	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648354	0.81[ASN][1000 genomes]
rs1351094	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17278571	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1904104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2126854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2306177	0.81[ASN][1000 genomes]
rs28785287	0.94[EUR][1000 genomes]
rs2903701	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs57275697	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836107	0.83[ASN][1000 genomes]
rs6845472	1.00[CEU][hapmap]
rs6845588	0.81[ASN][1000 genomes]
rs6847297	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6851699	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7683530	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2867919	RCHY1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76392600-76434800	Weak transcription	Gastric	stomach
2	chr4:76394000-76406200	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:76394000-76406600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:76394600-76424600	Weak transcription	Right Ventricle	heart
5	chr4:76395400-76405200	Weak transcription	Fetal Heart	heart
6	chr4:76395600-76405800	Weak transcription	Brain Germinal Matrix	brain
7	chr4:76395800-76406600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
9	chr4:76395800-76437000	Weak transcription	Lung	lung
10	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
11	chr4:76396200-76424400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
13	chr4:76396600-76403600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:76397000-76403400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:76397000-76403600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:76397000-76405200	Weak transcription	NHEK	skin
17	chr4:76397200-76403600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:76397200-76403800	Weak transcription	HUVEC	blood vessel
19	chr4:76397200-76405200	Weak transcription	Left Ventricle	heart
20	chr4:76397200-76414600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:76397400-76403600	Weak transcription	NH-A	brain
22	chr4:76397400-76403800	Weak transcription	GM12878-XiMat	blood
23	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:76398000-76403600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:76398200-76405600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:76398200-76415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:76398200-76434200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:76398400-76407400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr4:76398600-76403600	Weak transcription	NHDF-Ad	bronchial
30	chr4:76398600-76405600	Weak transcription	NHLF	lung
31	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:76399400-76434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr4:76400600-76403600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:76400600-76403800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
36	chr4:76400800-76404800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:76400800-76405200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:76400800-76405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:76400800-76405600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:76400800-76406600	Weak transcription	HMEC	breast
41	chr4:76400800-76409200	Weak transcription	Thymus	Thymus
42	chr4:76401000-76405400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:76401000-76405400	Weak transcription	Colonic Mucosa	Colon
44	chr4:76401000-76406600	Weak transcription	Hela-S3	cervix
45	chr4:76401000-76410800	Weak transcription	HSMMtube	muscle
46	chr4:76401000-76436200	Weak transcription	Brain Angular Gyrus	brain
47	chr4:76401200-76403800	Weak transcription	Fetal Intestine Large	intestine
48	chr4:76401200-76405200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:76401200-76405200	Weak transcription	Brain Substantia Nigra	brain
50	chr4:76401200-76406000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links